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(-) Description

Title :  X-RAY STRUCTURE OF ENHANCED GREEN FLUORESCENT PROTEIN (EGFP)
 
Authors :  A. Royant, M. Noirclerc-Savoye
Date :  02 Dec 10  (Deposition) - 27 Apr 11  (Release) - 27 Apr 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Fluorescent Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Royant, M. Noirclerc-Savoye
Stabilizing Role Of Glutamic Acid 222 In The Structure Of Enhanced Green Fluorescent Protein.
J. Struct. Biol. V. 174 385 2011
PubMed-ID: 21335090  |  Reference-DOI: 10.1016/J.JSB.2011.02.004

(-) Compounds

Molecule 1 - GREEN FLUORESCENT PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PLX02
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: STAR
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: AEQUOREA VICTORIA
    Organism Taxid: 6100
    Other Details: CHROMOPHORE RESULTING FROM AUTOCATALYTIC CYCLIZATION OF CONSECUTIVE AMINO ACID RESIDUES THR65, TYR66 AND GLY67.

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1CRO1Mod. Amino Acid{2-[(1R,2R)-1-AMINO-2-HYDROXYPROPYL]-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC ACID

(-) Sites  (0, 0)

(no "Site" information available for 2Y0G)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Y0G)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Met A:88 -Pro A:89

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (4, 4)

Asymmetric/Biological Unit (4, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_GFP_AEQVI_001 *F100YGFP_AEQVI  ---  ---AF100Y
2UniProtVAR_GFP_AEQVI_002 *T108SGFP_AEQVI  ---  ---AT108S
3UniProtVAR_GFP_AEQVI_003 *L141MGFP_AEQVI  ---  ---AL141M
4UniProtVAR_GFP_AEQVI_004 *V219IGFP_AEQVI  ---  ---AV219I
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Y0G)

(-) Exons   (0, 0)

(no "Exon" information available for 2Y0G)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:226
 aligned with GFP_AEQVI | P42212 from UniProtKB/Swiss-Prot  Length:238

    Alignment length:228
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222        
            GFP_AEQVI     3 KGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTFSYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGIT 230
               SCOP domains d2y0ga_ A: automated matches                                                                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains --GFP-2y0gA01 A:5-229                                                                                                                                                                                                              - Pfam domains
         Sec.struct. author hhhhhhh..eeeeeeeeeee..eeeeeeeeeeeehhh.eeeeeeee.......hhhhhh...-.-hhhhh..hhhhhhhhhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee....................eeeeeeehhhheeeeeeeeeee.....eeeeeeeeeeee...........eeeeeeeeee........eeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------Y-------S--------------------------------M-----------------------------------------------------------------------------I----------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2y0g A   3 KGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTL-s-VQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGIT 230
                                    12        22        32        42        52        62 | | |  72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222        
                                                                                        64 | |                                                                                                                                                                  
                                                                                          66-CRO                                                                                                                                                                
                                                                                            68
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2Y0G)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: GFP (101)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (GFP_AEQVI | P42212)
molecular function
    GO:0003674    molecular_function    Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
biological process
    GO:0008218    bioluminescence    The production of light by certain enzyme-catalyzed reactions in cells.
    GO:0006091    generation of precursor metabolites and energy    The chemical reactions and pathways resulting in the formation of precursor metabolites, substances from which energy is derived, and any process involved in the liberation of energy from these substances.
    GO:0018298    protein-chromophore linkage    The covalent or noncovalent attachment of a chromophore to a protein.
cellular component
    GO:0005575    cellular_component    The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.

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  Cis Peptide Bonds
    Met A:88 - Pro A:89   [ RasMol ]  
 

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  2y0g
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  GFP_AEQVI | P42212
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        GFP_AEQVI | P42212: 1b9c 1bfp 1c4f 1cv7 1ema 1emb 1emc 1eme 1emf 1emg 1emk 1eml 1emm 1f09 1f0b 1gfl 1h6r 1hcj 1huy 1jby 1jbz 1jc0 1jc1 1kp5 1kyp 1kyr 1kys 1myw 1q4a 1q4b 1q4c 1q4d 1q4e 1q73 1qxt 1qy3 1qyf 1qyo 1qyq 1rm9 1rmm 1rmo 1rmp 1rrx 1s6z 1w7s 1w7t 1w7u 1yfp 1yhg 1yhh 1yhi 1yj2 1yjf 1z1p 1z1q 2ah8 2aha 2awj 2awk 2awl 2awm 2b3p 2b3q 2due 2duf 2dug 2duh 2dui 2emd 2emn 2emo 2fwq 2fzu 2g16 2g2s 2g3d 2g5z 2g6e 2h6v 2h9w 2hcg 2hfc 2hgd 2hgy 2hjo 2hqz 2hrs 2jad 2o24 2o29 2o2b 2okw 2oky 2q57 2q6p 2qrf 2qt2 2qu1 2qz0 2wsn 2wso 2wur 2ydz 2ye0 2ye1 2yfp 3cb9 3cbe 3cd1 3cd9 3dpw 3dpx 3dpz 3dq1 3dq2 3dq3 3dq4 3dq5 3dq6 3dq7 3dq8 3dq9 3dqa 3dqc 3dqd 3dqe 3dqf 3dqh 3dqi 3dqj 3dqk 3dql 3dqm 3dqn 3dqo 3dqu 3ed8 3ek4 3ek7 3ek8 3ekh 3ekj 3evp 3evr 3evu 3evv 3g9a 3gex 3gj1 3gj2 3i19 3k1k 3la1 3o77 3o78 3ogo 3osq 3osr 3p28 3sg2 3sg3 3sg4 3sg5 3sg6 3sg7 3sry 3ss0 3ssh 3ssk 3ssl 3ssp 3sst 3ssv 3ssy 3st0 3sv5 3svb 3svc 3svd 3sve 3u8p 3ufz 3ug0 3v3d 3vht 3w1c 3w1d 3wlc 3wld 3ztf 4anj 4ar7 4as8 4b5y 4bdu 4en1 4eul 4ges 4gf6 4h47 4h48 4ik1 4ik3 4ik4 4ik5 4ik8 4ik9 4j88 4j89 4j8a 4jfg 4jrb 4ka9 4kag 4kex 4kf5 4kw4 4kw8 4kw9 4l12 4l13 4l1i 4lqt 4lqu 4lw5 4n3d 4ndj 4ndk 4ogs 4orn 4p1q 4p7h 4pa0 4pfe 4u2v 4xbi 4xgy 4xl5 4xov 4xow 4xvp 4z4k 4z4m 4zf3 4zf4 4zf5 5aqb 5dpg 5dph 5dpi 5dpj 5dqb 5dqm 5drf 5drg 5dtx 5dty 5dtz 5du0 5ehu 5f9g 5fgu 5fji 5hbd 5hge 5hw9 5hzo 5j2o 5j3n 5ktg 5t3i

(-) Related Entries Specified in the PDB File

1b9c GREEN FLUORESCENT PROTEIN MUTANT F99S, M153T AND V163A
1bfp BLUE VARIANT OF GREEN FLUORESCENT PROTEIN
1c4f GREEN FLUORESCENT PROTEIN S65T AT PH 4.6
1cv7 CRYSTAL STRUCTURE OF ENHANCED CYAN-EMISSION VARIANT OF GFP
1ema GREEN FLUORESCENT PROTEIN FROM AEQUOREA VICTORIA
1emb GREEN FLUORESCENT PROTEIN (GFP) FROM AEQUOREAVICTORIA, GLN 80 REPLACED WITH ARG
1emc GREEN FLUORESCENT PROTEIN FROM AEQUOREA VICTORIA, MUTANT
1eme GREEN FLUORESCENT PROTEIN FROM AEQUOREA VICTORIA, MUTANT
1emf GREEN FLUORESCENT PROTEIN FROM AEQUOREA VICTORIA, MUTANT
1emg GREEN FLUORESCENT PROTEIN (65-67 REPLACED BY CRO, S65TSUBSTITUTION, Q80R)
1emk GREEN FLUORESCENT PROTEIN FROM AEQUOREA VICTORIA, MUTANT
1eml GREEN FLUORESCENT PROTEIN FROM AEQUOREA VICTORIA, MUTANT
1emm GREEN FLUORESCENT PROTEIN FROM AEQUOREA VICTORIA, MUTANT
1f09 CRYSTAL STRUCTURE OF THE GREEN FLUORESCENT PROTEIN (GFP)VARIANT YFP-H148Q WITH TWO BOUND IODIDES
1f0b CRYSTAL STRUCTURE OF THE GREEN FLUORESCENT PROTEIN (GFP)VARIANT YFP-H148Q
1gfl STRUCTURE OF GREEN FLUORESCENT PROTEIN
1h6r A REDOX SENSITIVE VARIANT OF GREEN FLUORESCENT PROTEIN
1hcj PHOTOPRODUCT OF THE WILD-TYPE AEQUOREA VICTORIA GREEN FLUORESCENT PROTEIN
1huy CRYSTAL STRUCTURE OF CITRINE, AN IMPROVED YELLOW VARIANT OFGREEN FLUORESCENT PROTEIN
1jby CRYSTAL STRUCTURE ANALYSIS OF A DUAL- WAVELENGTH EMISSIONGREEN FLUORESCENT PROTEIN VARIANT AT LOW PH
1jbz CRYSTAL STRUCTURE ANALYSIS OF A DUAL- WAVELENGTH EMISSIONGREEN FLUORESCENT PROTEIN VARIANT AT HIGH PH
1jc0 CRYSTAL STRUCTURE ANALYSIS OF A REDOX- SENSITIVE GREENFLUORESCENT PROTEIN VARIANT IN A REDUCED FORM
1jc1 CRYSTAL STRUCTURE ANALYSIS OF A REDOX- SENSITIVE GREENFLUORESCENT PROTEIN VARIANT IN A OXIDIZED FORM
1kp5 CYCLIC GREEN FLUORESCENT PROTEIN
1kyp CRYSTAL STRUCTURE OF AN APO GREEN FLUORESCENT PROTEIN ZNBIOSENSOR
1kyr CRYSTAL STRUCTURE OF A CU-BOUND GREEN FLUORESCENT PROTEINZN BIOSENSOR
1kys CRYSTAL STRUCTURE OF A ZN-BOUND GREEN FLUORESCENT PROTEINBIOSENSOR
1myw CRYSTAL STRUCTURE OF A YELLOW FLUORESCENT PROTEIN WITHIMPROVED MATURATION AND REDUCED ENVIRONMENTAL SENSITIVITY
1q4a S65T Q80R GREEN FLUORESCENT PROTEIN (GFP) PH 8.5
1q4b S65T Q80R GREEN FLUORESCENT PROTEIN (GFP) PH 5.5
1q4c S65T Q80R T203C GREEN FLUORESCENT PROTEIN ( GFP) PH 8.5
1q4d S65T Q80R T203C GREEN FLUORESCENT PROTEIN ( GFP) PH 5.5
1q4e S65T Q80R Y145C GREEN FLUORESCENT PROTEIN ( GFP) PH 8.5
1q73 S65T Q80R Y145C T203C GREEN FLUORESCENT PROTEIN (GFP) PH 8.5
1qxt CRYSTAL STRUCTURE OF PRECYCLIZED INTERMEDIATE FOR THE GREENFLUORESCENT PROTEIN R96A VARIANT (A)
1qy3 CRYSTAL STRUCTURE OF PRECYCLIZED INTERMEDIATE FOR THE GREENFLUORESCENT PROTEIN R96A VARIANT (B)
1qyf CRYSTAL STRUCTURE OF MATURED GREEN FLUORESCENT PROTEIN R96AVARIANT
1qyo ANAEROBIC PRECYLIZATION INTERMEDIATE CRYSTAL STRUCTURE FORS65G Y66G GFP VARIANT
1qyq CRYSTAL STRUCTURE OF THE CYCLIZED S65G Y66G GFP VARIANT
1rm9 PROBING THE ROLE OF TRYPTOPHANS IN AEQUOREA VICTORIA GREENFLUORESCENT PROTEINS WITH AN EXPANDED GENETIC CODE
1rmm PROBING THE ROLE OF TRYPTOPHANS IN AEQUOREA VICTORIA GREENFLUORESCENT PROTEINS WITH AN EXPANDED GENETIC CODE
1rmo PROBING THE ROLE OF TRYPTOPHANS IN AEQUOREA VICTORIA GREENFLUORESCENT PROTEINS WITH AN EXPANDED GENETIC CODE
1rmp PROBING THE ROLE OF TRYPTOPHANS IN AEQUOREA VICTORIA GREENFLUORESCENT PROTEINS WITH AN EXPANDED GENETIC CODE
1rrx CRYSTALLOGRAPHIC EVIDENCE FOR ISOMERIC CHROMOPHORES IN 3-FLUOROTYROSYL-GREEN FLUORESCENT PROTEIN
1w7s WILD-TYPE AEQUOREA VICTORIA GREEN FLUORESCENT PROTEIN
1w7t PHOTOPRODUCT OF THE WILD-TYPE AEQUOREA VICTORIA GREEN FLUORESCENT PROTEIN AT 100 K
1w7u PHOTOPRODUCT OF THE WILD-TYPE AEQUOREA VICTORIA GREEN FLUORESCENT PROTEIN AFTER STRUCTURAL ANNEALING AT 170K
1yfp STRUCTURE OF YELLOW-EMISSION VARIANT OF GFP
1yhg UNCYCLIZED PRECURSOR STRUCTURE OF S65G Y66S V68G GFP VARIANT
1yhh UNCYCLIZED PRECURSOR STRUCTURE OF S65A Y66S G67A GFP VARIANT
1yhi UNCYCLIZED PRECURSOR STRUCTURE OF S65A Y66S R96A GFP VARIANT
1yj2 CYCLIZED, NON-DEHYDRATED POST-TRANSLATIONAL PRODUCT FORS65A Y66S H148G GFP VARIANT
1yjf CYCLIZED POST-TRANSLATIONAL PRODUCT FOR S65A Y66S (GFPHAL)GREEN FLUORESCENT PROTEIN VARIANT
1z1p Y66L VARIANT OF ENHANCED GREEN FLUORESCENT PROTEIN WITH 412-NM ABSORBING CHROMOPHORE
1z1q Y66L VARIANT OF ENHANCED GREEN FLUORESCENT PROTEIN WITH 374-NM ABSORBING CHROMOPHORE
2ah8 ROGFP1-R7. CYSTAL STRUCTURE ANALYSIS OF A RATE-ENHANCEDVARIANT OF REDOX-SENSITIVE GREEN FLUORESCENT PROTEIN INTHE OXIDIZED FORM.
2aha ROGFP1-R8. CYSTAL STRUCTURE ANALYSIS OF A RATE-ENHANCEDVARIANT OF REDOX-SENSITIVE GREEN FLUORESCENT PROTEIN INTHE REDUCED FORM.
2b3p CRYSTAL STRUCTURE OF A SUPERFOLDER GREEN FLUORESCENT PROTEIN
2b3q CRYSTAL STRUCTURE OF A WELL-FOLDED VARIANT OF GREENFLUORESCENT PROTEIN
2emd GREEN FLUORESCENT PROTEIN FROM AEQUOREA VICTORIA, MUTANT
2emn GREEN FLUORESCENT PROTEIN FROM AEQUOREA VICTORIA, MUTANT
2emo GREEN FLUORESCENT PROTEIN FROM AEQUOREA VICTORIA, MUTANT
2fwq REDUCED ENOLATE CHROMOPHORE INTERMEDIATE FOR Y66H GFPVARIANT
2fzu REDUCED ENOLATE CHROMOPHORE INTERMEDIATE FOR GFP VARIANT
2wsn STRUCTURE OF ENHANCED CYAN FLUORESCENT PROTEIN AT PHYSIOLOGICAL PH
2wso STRUCTURE OF CERULEAN FLUORESCENT PROTEIN AT PHYSIOLOGICAL PH
2wur ATOMIC RESOLUTION STRUCTURE OF GFP MEASURED ON A ROTATING ANODE
2yfp STRUCTURE OF YELLOW-EMISSION VARIANT OF GFP